The Experts below are selected from a list of 8184 Experts worldwide ranked by ideXlab platform
Vanden Broeck Jozef - One of the best experts on this subject based on the ideXlab platform.
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Extracellular vesicles spread the RNA interference signal of Tribolium castaneum TcA cells
'Elsevier BV', 2020Co-Authors: Wynant Niels, Santos Dulce, Peeters Paulien, Mingels Lina, Gansemans Yannick, Billen Johan, Van Nieuwerburgh Filip, Vanden Broeck JozefAbstract:The potential utility of RNA interference (RNAi) to control insect pests and viral infections depends largely on the target organism's ability to systemically spread the RNAi response. The efficacy of systemic RNAi varies among insects, though it has been shown to be high in the red flour beetle, Tribolium castaneum. We identified an extracellular RNAi signal that is present in the culture medium of T. castaneum (TcA) cells after treatment with long dsRNA specific for a luciferase reporter gene. Luciferase-specific siRNAs were detected in extracellular vesicles (EVs) that were purified from the culture medium of these dsRNA-treated cells. Furthermore, by measuring the silencing of luciferase expression, we showed that these siRNA-containing EVs can act as an RNAi signal for recipient TcA cells. We have therefore shown that a systemic RNAi response upon dsRNA treatment can be effectively spread through EVs.status: Published onlin
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Extracellular vesicles spread the RNA interference signal of Tribolium castaneum TcA cells
'Elsevier BV', 2020Co-Authors: Wynant Niels, Santos Dulce, Peeters Paulien, Mingels Lina, Gansemans Yannick, Billen Johan, Van Nieuwerburgh Filip, Vanden Broeck JozefAbstract:The potential utility of RNA interference (RNAi) to control insect pests and viral infections depends largely on the target organism's ability to systemically spread the RNAi response. The efficacy of systemic RNAi varies among insects, though it has been shown to be high in the red flour beetle, Tribolium castaneum. We identified an extracellular RNAi signal that is present in the culture medium of T. castaneum (TcA) cells after treatment with long dsRNA specific for a luciferase reporter gene. Luciferase-specific siRNAs were detected in extracellular vesicles (EVs) that were purified from the culture medium of these dsRNA-treated cells. Furthermore, by measuring the silencing of luciferase expression, we showed that these siRNA-containing EVs can act as an RNAi signal for recipient TcA cells. We have therefore shown that a systemic RNAi response upon dsRNA treatment can be effectively spread through EVs
Richard W Beeman - One of the best experts on this subject based on the ideXlab platform.
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beetlebase in 2010 revisions to provide comprehensive genomic information for Tribolium castaneum
Nucleic Acids Research, 2010Co-Authors: Hee Shin Kim, Marce D Lorenzen, Richard W Beeman, Terence Murphy, Jing Xia, Doina Caragea, Yoonseong Park, Stephen Butcher, Robert J Manak, Susan J BrownAbstract:BeetleBase (http://www.beetlebase.org) has been updated to provide more comprehensive genomic information for the red flour beetle Tribolium castaneum. The database contains genomic sequence scaffolds mapped to 10 linkage groups (genome assembly release Tcas_3.0), genetic linkage maps, the official gene set, Reference Sequences from NCBI (RefSeq), predicted gene models, ESTs and whole-genome tiling array data representing several developmental stages. The database was reconstructed using the upgraded Generic Model Organism Database (GMOD) modules. The genomic data is stored in a PostgreSQL relatational database using the Chado schema and visualized as tracks in GBrowse. The updated genetic map is visualized using the comparative genetic map viewer CMAP. To enhance the database search capabilities, the BLAST and BLAT search tools have been integrated with the GMOD tools. BeetleBase serves as a long-term repository for Tribolium genomic data, and is compatible with other model organism databases.
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characterization and expression of the β n acetylhexosaminidase gene family of Tribolium castaneum
Insect Biochemistry and Molecular Biology, 2008Co-Authors: David G Hogenkamp, Yasuyuki Arakane, Karl J Kramer, Subbaratnam Muthukrishnan, Richard W BeemanAbstract:Abstract Enzymes belonging to the β-N-acetylhexosaminidase family cleave chitin oligosaccharides produced by the action of chitinases on chitin into the constituent N-acetylglucosamine monomer. Four genes encoding putative chitooligosaccharidolytic β-N-acetylhexosaminidases (hereafter referred to as N-acetylglucosaminidases (NAGs)) in the red flour beetle, Tribolium castaneum, namely TcNAG1, TcFDL, TcNAG2, and TcNAG3, and three other related hexosaminidases were identified by searching the recently completed genome [Tribolium Genome Sequencing Consortium, 2007. The first genome sequence of a beetle, Tribolium castaneum, a model for insect development and pest biology. Nature, submitted for publication]. Full-length cDNAs for all four NAGs were cloned and sequenced, and the exon–intron organization of the corresponding genes was determined. Analyses of their developmental expression patterns indicated that, although all four of the NAGs are transcribed during most developmental stages, each gene had a distinct spatial and temporal expression pattern. TcNAG1 transcripts are the most abundant, particularly at the late pupal stage, while TcNAG3 transcripts are the least abundant, even at their peak levels in the late larval stages. The function of each NAG during different developmental stages was assessed by observations of lethal phenotypes after gene-specific double-stranded RNA (dsRNA)-mediated transcript depletion as verified by real-time PCR. TcNAG1 dsRNA was most effective in interrupting all three types of molts: larval–larval, larval–pupal, and pupal–adult. Treated insects died after failing to completely shed their old cuticles. Knockdown of transcripts for the other three NAG genes resulted in phenotypes similar to those of TcNAG1 dsRNA-treated insects, but the effects were somewhat variable and less severe. Sequence comparisons with other enzymatically characterized insect homologs suggested that TcFDL, unlike the other NAGs, may have a role in N-glycan processing in addition to its apparent role in cuticular chitin turnover. These results support the hypothesis that TcNAGs participate in chitin turnover and/or N-glycan processing during insect development and that each NAG fulfills an essential and distinct function.
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analysis of transcriptome data in the red flour beetle Tribolium castaneum
Insect Biochemistry and Molecular Biology, 2008Co-Authors: Yoonseong Park, Marce D Lorenzen, Susan J Brown, Richard W Beeman, Jeffrey C Lord, Brenda Oppert, Stephen Richards, Jamie Aikins, Liangjiang Wang, George Matthew WeinstockAbstract:The whole genome sequence of Tribolium castaneum, a worldwide coleopteran pest of stored products, has recently been determined. In order to facilitate accurate annotation and detailed functional analysis of this genome, we have compiled and analyzed all available expressed sequence tag (EST) data. The raw data consist of 61,228 ESTs, including 10,704 obtained from NCBI and an additional 50,524 derived from 32,544 clones generated in our laboratories. These sequences were amassed from cDNA libraries representing six different tissues or stages, namely: whole embryos, whole larvae, larval hindguts and Malpighian tubules, larval fat bodies and carcasses, adult ovaries, and adult heads. Assembly of the 61,228 sequences collapsed into 12,269 clusters (groups of overlapping ESTs representing single genes), of which 10,134 mapped onto 6463 (39%) of the 16,422 GLEAN gene models (i.e. official Tribolium gene list). Approximately 1600 clusters (13% of the total) lack corresponding GLEAN models, despite high matches to the genome, suggesting that a considerable number of transcribed sequences were missed by the gene prediction programs or were removed by GLEAN. We conservatively estimate that the current EST set represents more than 7500 transcription units.
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piggybac based insertional mutagenesis in Tribolium castaneum using donor helper hybrids
Insect Molecular Biology, 2007Co-Authors: Marce D Lorenzen, T Kimzey, Teresa D Shippy, Susan J Brown, Robin E Denell, Richard W BeemanAbstract:We describe an efficient method for generating new piggyBac insertions in the germline of F 1 hybrid Tribolium castaneum derived from crosses between transgenic helper and donor strains. Helper strains carried single Minos elements encoding piggyBac transposase. The donor strain carried a single piggyBac element inserted into an actin gene, expanding the eye-specific, 3xP3-EGFP (enhanced green fluorescent protein) reporter expression domain to include muscle. Remobilization of the donor element is accompanied by loss of muscle fluorescence but retention of eye fluorescence. In a pilot screen, the piggyBac donor was remobilized in 84% of the hybrid crosses, generating hundreds of new lethal, enhancer-trap, semisterile and other insertions. The jumpstarter system described herein makes genome-wide, saturation insertional mutagenesis a realistic goal in this coleopteran species.
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piggybac mediated germline transformation in the beetle Tribolium castaneum
Insect Molecular Biology, 2003Co-Authors: Marce D Lorenzen, Susan J Brown, Robin E Denell, Martin Klingler, Andreas J Berghammer, Richard W BeemanAbstract:The lepidopteran transposable element piggyBac can mediate germline insertions in at least four insect orders. It therefore shows promise as a broad-spectrum transformation vector, but applications such as enhancer trapping and transposon-tag mutagenesis are still lacking. We created, cloned, sequenced and genetically mapped a set of piggyBac insertions in the red flour beetle, Tribolium castaneum. Transpositions were precise, and specifically targeted the canonical TTAA recognition sequence. We detected several novel reporter-expression domains, indicating that piggyBac could be used to identify enhancer regions. We also demonstrated that a primary insertion of a non-autonomous element can be efficiently remobilized to non-homologous chromosomes by injection of an immobile helper element into embryos harbouring the primary insertion. These developments suggest potential for more sophisticated methods of piggyBac-mediated genome manipulation.
Mingels Lina - One of the best experts on this subject based on the ideXlab platform.
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Extracellular vesicles spread the RNA interference signal of Tribolium castaneum TcA cells
'Elsevier BV', 2020Co-Authors: Wynant Niels, Santos Dulce, Peeters Paulien, Mingels Lina, Gansemans Yannick, Billen Johan, Van Nieuwerburgh Filip, Vanden Broeck JozefAbstract:The potential utility of RNA interference (RNAi) to control insect pests and viral infections depends largely on the target organism's ability to systemically spread the RNAi response. The efficacy of systemic RNAi varies among insects, though it has been shown to be high in the red flour beetle, Tribolium castaneum. We identified an extracellular RNAi signal that is present in the culture medium of T. castaneum (TcA) cells after treatment with long dsRNA specific for a luciferase reporter gene. Luciferase-specific siRNAs were detected in extracellular vesicles (EVs) that were purified from the culture medium of these dsRNA-treated cells. Furthermore, by measuring the silencing of luciferase expression, we showed that these siRNA-containing EVs can act as an RNAi signal for recipient TcA cells. We have therefore shown that a systemic RNAi response upon dsRNA treatment can be effectively spread through EVs.status: Published onlin
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Extracellular vesicles spread the RNA interference signal of Tribolium castaneum TcA cells
'Elsevier BV', 2020Co-Authors: Wynant Niels, Santos Dulce, Peeters Paulien, Mingels Lina, Gansemans Yannick, Billen Johan, Van Nieuwerburgh Filip, Vanden Broeck JozefAbstract:The potential utility of RNA interference (RNAi) to control insect pests and viral infections depends largely on the target organism's ability to systemically spread the RNAi response. The efficacy of systemic RNAi varies among insects, though it has been shown to be high in the red flour beetle, Tribolium castaneum. We identified an extracellular RNAi signal that is present in the culture medium of T. castaneum (TcA) cells after treatment with long dsRNA specific for a luciferase reporter gene. Luciferase-specific siRNAs were detected in extracellular vesicles (EVs) that were purified from the culture medium of these dsRNA-treated cells. Furthermore, by measuring the silencing of luciferase expression, we showed that these siRNA-containing EVs can act as an RNAi signal for recipient TcA cells. We have therefore shown that a systemic RNAi response upon dsRNA treatment can be effectively spread through EVs
George Matthew Weinstock - One of the best experts on this subject based on the ideXlab platform.
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analysis of transcriptome data in the red flour beetle Tribolium castaneum
Insect Biochemistry and Molecular Biology, 2008Co-Authors: Yoonseong Park, Marce D Lorenzen, Susan J Brown, Richard W Beeman, Jeffrey C Lord, Brenda Oppert, Stephen Richards, Jamie Aikins, Liangjiang Wang, George Matthew WeinstockAbstract:The whole genome sequence of Tribolium castaneum, a worldwide coleopteran pest of stored products, has recently been determined. In order to facilitate accurate annotation and detailed functional analysis of this genome, we have compiled and analyzed all available expressed sequence tag (EST) data. The raw data consist of 61,228 ESTs, including 10,704 obtained from NCBI and an additional 50,524 derived from 32,544 clones generated in our laboratories. These sequences were amassed from cDNA libraries representing six different tissues or stages, namely: whole embryos, whole larvae, larval hindguts and Malpighian tubules, larval fat bodies and carcasses, adult ovaries, and adult heads. Assembly of the 61,228 sequences collapsed into 12,269 clusters (groups of overlapping ESTs representing single genes), of which 10,134 mapped onto 6463 (39%) of the 16,422 GLEAN gene models (i.e. official Tribolium gene list). Approximately 1600 clusters (13% of the total) lack corresponding GLEAN models, despite high matches to the genome, suggesting that a considerable number of transcribed sequences were missed by the gene prediction programs or were removed by GLEAN. We conservatively estimate that the current EST set represents more than 7500 transcription units.
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The genome of the model beetle and pest Tribolium castaneum
Nature, 2008Co-Authors: Stephen Richards, R. Gibbs, George Matthew Weinstock, Susan Brown, R. Denell, R. Beeman, G. Bucher, A. ChaumotAbstract:Tribolium castaneum is a member of the most species-rich eukaryotic order, a powerful model organism for the study of generalized insect development, and an important pest of stored agricultural products. We describe its genome sequence here. This omnivorous beetle has evolved the ability to interact with a diverse chemical environment, as shown by large expansions in odorant and gustatory receptors, as well as P450 and other detoxification enzymes. Development in Tribolium is more representative of other insects than is Drosophila, a fact reflected in gene content and function. For example, Tribolium has retained more ancestral genes involved in cellcell communication than Drosophila, some being expressed in the growth zone crucial for axial elongation in short-germ development. Systemic RNA interference in T. castaneum functions differently from that in Caenorhabditis elegans, but nevertheless offers similar power for the elucidation of gene function and identification of targets for selective insect control.
Susan J Brown - One of the best experts on this subject based on the ideXlab platform.
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beetlebase in 2010 revisions to provide comprehensive genomic information for Tribolium castaneum
Nucleic Acids Research, 2010Co-Authors: Hee Shin Kim, Marce D Lorenzen, Richard W Beeman, Terence Murphy, Jing Xia, Doina Caragea, Yoonseong Park, Stephen Butcher, Robert J Manak, Susan J BrownAbstract:BeetleBase (http://www.beetlebase.org) has been updated to provide more comprehensive genomic information for the red flour beetle Tribolium castaneum. The database contains genomic sequence scaffolds mapped to 10 linkage groups (genome assembly release Tcas_3.0), genetic linkage maps, the official gene set, Reference Sequences from NCBI (RefSeq), predicted gene models, ESTs and whole-genome tiling array data representing several developmental stages. The database was reconstructed using the upgraded Generic Model Organism Database (GMOD) modules. The genomic data is stored in a PostgreSQL relatational database using the Chado schema and visualized as tracks in GBrowse. The updated genetic map is visualized using the comparative genetic map viewer CMAP. To enhance the database search capabilities, the BLAST and BLAT search tools have been integrated with the GMOD tools. BeetleBase serves as a long-term repository for Tribolium genomic data, and is compatible with other model organism databases.
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analysis of transcriptome data in the red flour beetle Tribolium castaneum
Insect Biochemistry and Molecular Biology, 2008Co-Authors: Yoonseong Park, Marce D Lorenzen, Susan J Brown, Richard W Beeman, Jeffrey C Lord, Brenda Oppert, Stephen Richards, Jamie Aikins, Liangjiang Wang, George Matthew WeinstockAbstract:The whole genome sequence of Tribolium castaneum, a worldwide coleopteran pest of stored products, has recently been determined. In order to facilitate accurate annotation and detailed functional analysis of this genome, we have compiled and analyzed all available expressed sequence tag (EST) data. The raw data consist of 61,228 ESTs, including 10,704 obtained from NCBI and an additional 50,524 derived from 32,544 clones generated in our laboratories. These sequences were amassed from cDNA libraries representing six different tissues or stages, namely: whole embryos, whole larvae, larval hindguts and Malpighian tubules, larval fat bodies and carcasses, adult ovaries, and adult heads. Assembly of the 61,228 sequences collapsed into 12,269 clusters (groups of overlapping ESTs representing single genes), of which 10,134 mapped onto 6463 (39%) of the 16,422 GLEAN gene models (i.e. official Tribolium gene list). Approximately 1600 clusters (13% of the total) lack corresponding GLEAN models, despite high matches to the genome, suggesting that a considerable number of transcribed sequences were missed by the gene prediction programs or were removed by GLEAN. We conservatively estimate that the current EST set represents more than 7500 transcription units.
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piggybac based insertional mutagenesis in Tribolium castaneum using donor helper hybrids
Insect Molecular Biology, 2007Co-Authors: Marce D Lorenzen, T Kimzey, Teresa D Shippy, Susan J Brown, Robin E Denell, Richard W BeemanAbstract:We describe an efficient method for generating new piggyBac insertions in the germline of F 1 hybrid Tribolium castaneum derived from crosses between transgenic helper and donor strains. Helper strains carried single Minos elements encoding piggyBac transposase. The donor strain carried a single piggyBac element inserted into an actin gene, expanding the eye-specific, 3xP3-EGFP (enhanced green fluorescent protein) reporter expression domain to include muscle. Remobilization of the donor element is accompanied by loss of muscle fluorescence but retention of eye fluorescence. In a pilot screen, the piggyBac donor was remobilized in 84% of the hybrid crosses, generating hundreds of new lethal, enhancer-trap, semisterile and other insertions. The jumpstarter system described herein makes genome-wide, saturation insertional mutagenesis a realistic goal in this coleopteran species.
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piggybac mediated germline transformation in the beetle Tribolium castaneum
Insect Molecular Biology, 2003Co-Authors: Marce D Lorenzen, Susan J Brown, Robin E Denell, Martin Klingler, Andreas J Berghammer, Richard W BeemanAbstract:The lepidopteran transposable element piggyBac can mediate germline insertions in at least four insect orders. It therefore shows promise as a broad-spectrum transformation vector, but applications such as enhancer trapping and transposon-tag mutagenesis are still lacking. We created, cloned, sequenced and genetically mapped a set of piggyBac insertions in the red flour beetle, Tribolium castaneum. Transpositions were precise, and specifically targeted the canonical TTAA recognition sequence. We detected several novel reporter-expression domains, indicating that piggyBac could be used to identify enhancer regions. We also demonstrated that a primary insertion of a non-autonomous element can be efficiently remobilized to non-homologous chromosomes by injection of an immobile helper element into embryos harbouring the primary insertion. These developments suggest potential for more sophisticated methods of piggyBac-mediated genome manipulation.
